Summary of Study ST000220

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000050. The data can be accessed directly via it's Project DOI: 10.21228/M8RG6T This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000220
Study TitleSmall cell lung cancer metabolome (part II)
Study TypeComparison of normal, lung adenocarcinoma and SCLC tissue metabolomes
Study SummaryIn addition to the generation and analysis of metabolomics data on cell lines, samples of normal lung tissue, adenocarcinoma lung tissue and small cell lung carcinoma tissue (seven samples/group) were processed and evaluated metabolite profile differences under the scope of the pilot and feasibility study. These data can be correlated to the metabolite profiles defined in the SCLC and NSCLC cell lines and integrated with the ABPP-determined metabolic kinases to identify distinct metabolic signatures or biomarkers (?oncometabolites?) that distinguish small cell lung cancer from non-small cell lung cancer.
Institute
University of North Carolina
DepartmentSystems and Translational Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2015-06-26
Num Groups3
Total Subjects21
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Uploaded File Size58 G
Analysis Type DetailLC-MS
Release Date2016-07-08
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8RG6T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000050
Project DOI:doi: 10.21228/M8RG6T
Project Title:Small cell lung cancer metabolome
Project Type:Metabolomic profiling comparison between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), to define novel biomarkers for therapy, diagnostics and early detection.
Project Summary:The goal of this pilot project is to comprehensively evaluate metabolic underpinnings of small cell lung cancer (SCLC) and couple with proteome level measurements of global kinase and other enzyme level expression data to provide insight into the upstream signaling networks that may be driving the pathogenesis of SCLC. Alterations in cancer metabolism are increasingly realized as an emerging area of research and potentially offers new therapeutic strategies. As part of ongoing studies, we are employing a chemical biology platform, activity-based protein profiling (ABPP), to study the SCLC proteome. ABPP uses chemical probes that are directed against the active sites of enzymes to interrogate the functional state of enzymes in biological samples. We used ATP based probes to study differences in kinase and other ATP binding proteins between SCLC and non-small cell lung cancer (NSCLC). We used well curated lung cancer cell lines that facilitate functional analysis of key proteins and pathways. Interestingly, our preliminary data strongly implicates hyperactivated metabolic pathways in SCLC when compared to NSCLC cell lines. A strong signal of upregulated metabolic kinases and other proteins involved in glycolysis, pyruvate metabolism, and purine metabolism have been identified through this approach. However, whether the alterations in the protein levels identified through this proteomic based approach corresponds to altered levels of metabolites through metabolic pathways remains unclear. This new opportunity will allow us to profile SCLC for alterations in metabolism that can be compared to NSCLC. We will conduct metabolomics studies on our SCLC cell lines. Relationships between the underlying alterations in metabolic kinases and other signaling molecules and mechanisms promoting the aggressive phenotype of these SCLC tumors remain unclear. We will collaborate with the NIH Eastern Regional Comprehensive Metabolomics Resource Core at RTI International (RTI RCMRC) to enable metabolomic profiling and analysis of our existing cell lines and tumor tissues.
Institute:H. Lee Moffitt Cancer Center
Department:NCI-designated comprehensive cancer center
Last Name:Haura
First Name:Eric B.
Address:12902 Magnolia Drive, MRC 3 East
Email:eric.haura@moffitt.org
Phone:813-745-6827

Subject:

Subject ID:SU000239
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:Moffitt Cancer Center Tissue Core
Species Group:Human

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Histology Type Conformed - CAP
SA010716SF-100109-231142Adenocarcinoma, NOS
SA010717SF-100109-244079Adenocarcinoma, NOS
SA010718SF-100109-227718Adenocarcinoma, NOS
SA010719SF-120831-00062Adenocarcinoma, NOS
SA010720SF-100109-255622Adenocarcinoma, NOS
SA010721SF-100109-239012Adenocarcinoma, NOS
SA010722SF-100109-259700Adenocarcinoma, NOS
SA010736SF-110121-00073Combined small cell carcinoma
SA010723SF-100109-114720Normal
SA010724SF-100109-121711Normal
SA010725SF-100109-130034Normal
SA010726SF-100109-124896Normal
SA010727SF-100109-199550Normal
SA010728SF-100109-169058Normal
SA010729SF-100109-124904Normal
SA010734SF-100109-146730Small cell carcinoma
SA010730SF-100109-199546Small cell carcinoma, NOS
SA010731SF-100109-225118Small cell carcinoma, NOS
SA010732SF-100109-252159Small cell carcinoma, NOS
SA010733SF-110908-00016Small cell carcinoma, NOS
SA010735SF-100109-142930Small cell carcinoma, NOS
Showing results 1 to 21 of 21

Collection:

Collection ID:CO000227
Collection Summary:-
Sample Type:tissue
Collection Method:Snap frozen

Treatment:

Treatment ID:TR000247

Sample Preparation:

Sampleprep ID:SP000241
Sampleprep Summary:Pulverized tissue samples were incubated in 50:50 Acetonitrile:Water for 1 hr, vortexed and centrifuged. Supernatants were transferred to new tubes along with isotopocially labled internal standard and samples were lyophilized to dryness. Dried samples were resuspended in 95:5 Water:Methanol and an aliquot was transferred to autosampler vials forbroad spectrum metabolomics data analysis acquisition.
Processing Method:Pulverization of frozen tissue (performed at Moffitt and supplied to RTI)
Extraction Method:50:50 Acetonitrile:Water
Extract Storage:-80 C
Sample Resuspension:95:5 Water:Methanol
Sample Spiking:L-Tryptophan-d5
Organ:Lung

Combined analysis:

Analysis ID AN000325 AN000326
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity HSS T3 (100 x 2.1mm,1.8um) Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt-G2-Si Waters Synapt-G2-Si
Ion Mode POSITIVE NEGATIVE
Units Normalized abundance Normalized abundance

Chromatography:

Chromatography ID:CH000245
Instrument Name:Waters Acquity
Column Name:Waters Acquity HSS T3 (100 x 2.1mm,1.8um)
Column Pressure:6000-10000
Column Temperature:50 C
Flow Gradient:Time(min) Flow Rate %A %B Curve; 1. Initial 0.400 100.0 0.0; 2. 1.00 0.400 100.0 0.0 6;3. 16.00 0.400 0.0 100.0 6; 4. 20.00 0.400 0.0 100.0 6; 5. 22.00 0.400 100.0 0.0 6
Flow Rate:0.4 mL/min
Injection Temperature:8 C
Internal Standard:L-Tryptophan-d5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Analytical Time:22 min
Weak Wash Solvent Name:5%MeOH
Weak Wash Volume:1000 uL
Strong Wash Solvent Name:80%MeOH
Strong Wash Volume:1000 uL
Target Sample Temperature:8 C
Sample Loop Size:10 uL
Sample Syringe Size:100 uL
Randomization Order:Yes
Chromatography Type:Reversed phase

MS:

MS ID:MS000274
Analysis ID:AN000325
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:110 C
Capillary Voltage:1.0 kV
Collision Energy:4
Fragmentation Method:CID
Helium Flow:180
Ionization:ES+
Mass Accuracy:5 ppm
Source Temperature:110 C
Dataformat:Continuum
Desolvation Gas Flow:400 L/Hr
Desolvation Temperature:400 C
Resolution Setting:18000
Scan Range Moverz:50-1000 m/s
Scanning Cycle:1 s
Tube Lens Voltage:75
  
MS ID:MS000275
Analysis ID:AN000326
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:110 C
Capillary Voltage:1.0 kV
Collision Energy:4
Fragmentation Method:CID
Helium Flow:180
Ionization:ES-
Mass Accuracy:5 ppm
Source Temperature:110 C
Dataformat:Continuum
Desolvation Gas Flow:400 L/Hr
Desolvation Temperature:400 C
Resolution Setting:18000
Scan Range Moverz:50-1000 m/z
Scanning Cycle:1 s
Tube Lens Voltage:74
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